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Created with Raphaël 2.2.017Nov15121110987432131Oct28272625242120191817141312111076543230Sep29282726232221201615141312987652131Aug302625242322191817161512111098542129Jul28272625222120141312118654130Jun282724232221201716141310986532126May2524231918171613121110test code to make sure the tutorials on the core api page run okayAdded a button to show/hide all the tablesCorrect file name xref_config.iniChanges to UniProtDirectParser - it can be used by any speciesuseful script to get the external databases references for a gene or transcript using either the stable_id or the gene nameUpdates for allele schema changeModify the PATH in the script so that the Perl fromImproved the colouring system:qw() as a list is deprecated in 5.14 so we shouldn't do itload_XXXX() methods now return the number of adaptors which have appeared in the registry due to that method's invocation. This can be used to report success or failure to load databases.Improving the error handling of the DBI connection in load_registry_from_db(). We now report an error if it cannot connect to the MySQL DB and if it was not pingable. Hopefully this catches both erronious scenarios.UpdateUse latest exonerate.In generate_similarity_events(): Tighten rules for when to generateBeeeep! Change alignment model to ungapped from affine:local.Drop translation rescore penalty from 0.95 to 0.9, but raise non-mappedIn fetch_all_by_logic_name(): If the provided logic name does not existadded option -show_links to show the genes linked to for the xrefs if a name is givenanalyse the xref data in the core databases to find out how they were mappedmodifying get_DBAdaptor() to only throw an error if $no_alias_check was onadded fetch_all_by_name which gets all the xrefs that have the accession, display_label or synonym that is passed to it. external database source is optionalImproving error documentation for methods which now throw errorsIn get_alias(): Prompt user to investigate API version and DB version inLogical error spotted by jm18.merge in changes from ensembl-64 for retrieving non-reference slices. Don't need to supply a value for logappend, verbose, interactive and dry_run parameters*** empty log message ***misssing bracketperl -c IKMCParser.pmthat was carelessnolog should override other log paramsChanges to _slice_fetch: simpify SQL if slice is an SNP - only 1bp long.BaseFeatureAdaptor.pmUpdate some penalties and comments.added status KNOWN_BY_PROJECTION to sub is_knownHonour the exonerate_concurrent_jobs setting in the config filemake them executabledrosophila needs to add direct GO xrefs. Before this fix the linkage_types were missingdisconnect from production databasepopulate analysis and analysis description if it's not already stored in the dbdisconnect from production databaseTest will fail if run on non-deterministic data storage engines as we have 2 features with the queried for ditag_id